It’s unavoidable - once the cheese gets hot enough the steam will either force the liquid cheese out of existing holes, or it will make its own holes.
Make sure they are fresh out of the freezer when you put them in, as this lets the outside crisp up more before the inside becomes lava. Once you get close to the prescribed cooking time, you need to just sit in front of the oven door and watch them, and as soon as 2-3 break open, take the whole tray out